Atomistry » Manganese » PDB 4php-4qsf » 4qag
Atomistry »
  Manganese »
    PDB 4php-4qsf »
      4qag »

Manganese in PDB 4qag: Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase

Enzymatic activity of Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase

All present enzymatic activity of Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase:
2.7.7.49; 2.7.7.7; 3.1.13.2; 3.1.26.13;

Protein crystallography data

The structure of Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase, PDB code: 4qag was solved by D.M.Himmel, W.C.Ho, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.57 / 1.71
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 51.164, 51.164, 112.100, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 19

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase (pdb code 4qag). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase, PDB code: 4qag:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4qag

Go back to Manganese Binding Sites List in 4qag
Manganese binding site 1 out of 4 in the Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:46.8
occ:1.00
 O1 A:F95603 2.0 53.5 1.0
OD1 A:ASP549 2.1 53.8 1.0
O A:HOH711 2.2 42.3 1.0
OD1 A:ASP443 2.2 40.6 1.0
O A:HOH712 2.2 48.3 1.0
O2 A:F95603 2.2 48.5 1.0
C3 A:F95603 2.8 52.4 1.0
C4 A:F95603 2.9 52.2 1.0
CG A:ASP443 3.1 41.0 1.0
CG A:ASP549 3.2 52.9 1.0
OD2 A:ASP443 3.4 37.2 1.0
CB A:ASP549 3.6 50.2 1.0
MN A:MN602 3.7 42.1 1.0
OD2 A:ASP498 3.8 50.1 1.0
NE2 A:HIS539 4.1 64.8 1.0
C2 A:F95603 4.2 52.0 1.0
CA A:ASP549 4.2 46.6 1.0
C5 A:F95603 4.3 56.4 1.0
O A:GLY444 4.3 44.9 1.0
OD2 A:ASP549 4.3 59.7 1.0
CE1 A:HIS539 4.4 67.8 1.0
CB A:ASP443 4.6 34.3 1.0
O A:HOH731 4.6 53.7 1.0
O3 A:F95603 4.8 48.6 1.0
CG A:ASP498 4.9 40.2 1.0

Manganese binding site 2 out of 4 in 4qag

Go back to Manganese Binding Sites List in 4qag
Manganese binding site 2 out of 4 in the Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:42.1
occ:1.00
 OD1 A:ASP498 2.1 40.2 1.0
OE2 A:GLU478 2.1 46.5 1.0
OD2 A:ASP443 2.1 37.2 1.0
O1 A:F95603 2.1 53.5 1.0
OD2 A:ASP498 2.3 50.1 1.0
O3 A:F95603 2.5 48.6 1.0
CG A:ASP498 2.5 40.2 1.0
C3 A:F95603 3.0 52.4 1.0
CD A:GLU478 3.0 45.6 1.0
C2 A:F95603 3.1 52.0 1.0
CG A:ASP443 3.2 41.0 1.0
OE1 A:GLU478 3.2 46.3 1.0
C7 A:F95603 3.5 56.5 1.0
MN A:MN601 3.7 46.8 1.0
OD1 A:ASP443 3.7 40.6 1.0
O A:HOH701 3.7 37.6 1.0
O4 A:F95603 3.7 57.2 1.0
O A:HOH711 3.9 42.3 1.0
O A:HOH710 4.0 73.3 1.0
CB A:ASP498 4.1 39.4 1.0
O A:GLY444 4.2 44.9 1.0
C4 A:F95603 4.3 52.2 1.0
CG A:GLU478 4.4 40.7 1.0
CB A:ASP443 4.4 34.3 1.0
C1 A:F95603 4.5 57.8 1.0
N A:GLY444 4.5 34.5 1.0
O A:HOH712 4.5 48.3 1.0
CA A:ASP443 4.6 32.5 1.0
C A:ASP498 4.7 39.3 1.0
CA A:ASP498 4.8 36.7 1.0
O2 A:F95603 4.8 48.5 1.0
C8 A:F95603 4.8 59.6 1.0
O A:ASP498 4.9 42.9 1.0
N A:SER499 4.9 35.0 1.0

Manganese binding site 3 out of 4 in 4qag

Go back to Manganese Binding Sites List in 4qag
Manganese binding site 3 out of 4 in the Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn601

b:49.9
occ:1.00
 OD1 B:ASP549 2.1 53.0 1.0
O1 B:F95603 2.1 53.5 1.0
OD1 B:ASP443 2.2 45.0 1.0
O B:HOH717 2.2 58.2 1.0
O B:HOH705 2.2 50.1 1.0
O2 B:F95603 2.2 52.1 1.0
C3 B:F95603 2.9 58.6 1.0
C4 B:F95603 2.9 54.1 1.0
CG B:ASP443 3.2 47.2 1.0
CG B:ASP549 3.2 56.9 1.0
OD2 B:ASP443 3.4 42.3 1.0
MN B:MN602 3.6 45.3 1.0
CB B:ASP549 3.7 47.9 1.0
OD2 B:ASP498 3.9 47.8 1.0
O B:HOH718 3.9 85.9 1.0
NE2 B:HIS539 4.1 58.7 1.0
CA B:ASP549 4.2 49.5 1.0
C2 B:F95603 4.2 56.8 1.0
C5 B:F95603 4.2 59.9 1.0
OD2 B:ASP549 4.3 62.3 1.0
O B:GLY444 4.3 46.6 1.0
OG B:SER553 4.5 69.4 1.0
CB B:ASP443 4.5 39.4 1.0
CE1 B:HIS539 4.6 62.9 1.0
O B:HOH701 4.8 57.3 1.0
O3 B:F95603 4.8 55.1 1.0
CG B:ASP498 5.0 37.5 1.0
O B:ASP549 5.0 55.2 1.0
CD2 B:HIS539 5.0 62.7 1.0

Manganese binding site 4 out of 4 in 4qag

Go back to Manganese Binding Sites List in 4qag
Manganese binding site 4 out of 4 in the Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn602

b:45.3
occ:1.00
 O1 B:F95603 2.0 53.5 1.0
OD1 B:ASP498 2.1 42.9 1.0
OD2 B:ASP443 2.1 42.3 1.0
OE1 B:GLU478 2.1 43.3 1.0
OD2 B:ASP498 2.3 47.8 1.0
CG B:ASP498 2.5 37.5 1.0
O3 B:F95603 2.5 55.1 1.0
C3 B:F95603 2.9 58.6 1.0
CD B:GLU478 3.1 45.2 1.0
CG B:ASP443 3.1 47.2 1.0
C2 B:F95603 3.1 56.8 1.0
OE2 B:GLU478 3.3 45.4 1.0
OD1 B:ASP443 3.5 45.0 1.0
MN B:MN601 3.6 49.9 1.0
C7 B:F95603 3.6 55.4 1.0
O B:HOH705 3.7 50.1 1.0
O B:HOH704 3.8 41.0 1.0
O4 B:F95603 3.9 53.2 1.0
CB B:ASP498 4.0 40.8 1.0
C4 B:F95603 4.2 54.1 1.0
O B:GLY444 4.2 46.6 1.0
CB B:ASP443 4.3 39.4 1.0
C1 B:F95603 4.5 62.1 1.0
CG B:GLU478 4.5 39.4 1.0
N B:GLY444 4.5 38.6 1.0
O B:HOH717 4.6 58.2 1.0
CA B:ASP443 4.7 40.6 1.0
O2 B:F95603 4.7 52.1 1.0
C B:ASP498 4.8 41.1 1.0
CA B:ASP498 4.8 41.2 1.0
C8 B:F95603 4.9 60.3 1.0
O B:ASP498 4.9 42.8 1.0

Reference:

D.M.Himmel, N.S.Myshakina, T.Ilina, A.Van Ry, W.C.Ho, M.A.Parniak, E.Arnold. Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase and Structure-Activity Analysis of Inhibitor Analogs. J.Mol.Biol. V. 426 2617 2014.
ISSN: ISSN 0022-2836
PubMed: 24840303
DOI: 10.1016/J.JMB.2014.05.006
Page generated: Sat Oct 5 20:58:56 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy